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https://www.readbyqxmd.com/read/28087426/next-generation-sequencing-of-a-large-gene-panel-in-patients-initially-diagnosed-with-idiopathic-ventricular-fibrillation
#1
Marloes Visser, Dennis Dooijes, Jasper J van der Smagt, Jeroen F van der Heijden, Pieter A Doevendans, Peter Loh, Folkert W Asselbergs, Rutger J Hassink
BACKGROUND: Idiopathic ventricular fibrillation (IVF) is a rare primary cardiac arrhythmia syndrome that is diagnosed in a resuscitated cardiac arrest victim, with documented ventricular fibrillation, in whom no underlying cause is identified after comprehensive clinical evaluation. In some patients causative genetic mutations are detected which facilitate patient treatment and follow-up. The feasibility of next generation sequencing (NGS) has increased with its greater availability and decreasing costs...
January 10, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28081284/analysis-of-the-relationship-between-ribosomal-dna-its-sequences-and-active-components-in-rhodiola-plants
#2
D J Zhang, W T Yuan, M T Li, Y H Zhang
Rhodiola plants are a valuable resource in traditional Chinese medicine. The objective of this study was to evaluate the correlation between ribosomal DNA internal transcribed spacer (ITS) sequences and the three active components in Rhodiola plants. For this, we determined ITS sequence polymorphisms and the concentrations of active components salidroside, tyrosol, and gallic acid in different Rhodiola species from the Tibetan Plateau. In a total of 23 Rhodiola samples, 16 different haplotypes were defined based on their ITS sequences...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28079488/association-analysis-of-ank3-variants-with-bipolar-disorder-in-the-korean-population
#3
Chul-Hyun Cho, Soojin Kim, Dongho Geum, Heon-Jeong Lee
BACKGROUND: Bipolar disorder (BD) is a major psychiatric disorder characterized by alternating mood episodes, including major depressive, hypomanic, and manic episodes. Previous genetic studies of BD have reported several genes as potentially associated with BD. The ANK3 gene has been identified as a possible BD susceptibility gene in genome-wide association analyses. AIMS: The goal of the present study was to evaluate the association of ANK3 variants with BD in the Korean population...
January 12, 2017: Nordic Journal of Psychiatry
https://www.readbyqxmd.com/read/28078358/major-histocompatibility-complex-haplotyping-and-long-amplicon-allele-discovery-in-cynomolgus-macaques-from-chinese-breeding-facilities
#4
Julie A Karl, Michael E Graham, Roger W Wiseman, Katelyn E Heimbruch, Samantha M Gieger, Gaby G M Doxiadis, Ronald E Bontrop, David H O'Connor
Very little is currently known about the major histocompatibility complex (MHC) region of cynomolgus macaques (Macaca fascicularis; Mafa) from Chinese breeding centers. We performed comprehensive MHC class I haplotype analysis of 100 cynomolgus macaques from two different centers, with animals from different reported original geographic origins (Vietnamese, Cambodian, and Cambodian/Indonesian mixed-origin). Many of the samples were of known relation to each other (sire, dam, and progeny sets), making it possible to characterize lineage-level haplotypes in these animals...
January 11, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28077634/characterization-of-hcv-envelope-diversification-from-acute-to-chronic-infection-using-smrt-sequencing-within-a-sexually-transmitted-hepatitis-c-virus-cluster
#5
Cynthia K Y Ho, Jayna Raghwani, Sylvie Koekkoek, Richard H Liang, Jan T M Van der Meer, Marc Van Der Valk, Menno De Jong, Oliver G Pybus, Janke Schinkel, Richard Molenkamp
: In contrast to other available next generation sequencing platforms, Pacbio Single Molecule, Real-Time (SMRT) sequencing has the advantage of generating long reads, albeit with a relatively higher error rate in unprocessed data. Using this platform we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1680 nt) from individuals belonging to a cluster of sexually-transmitted cases. All five subjects were HIV-1 coinfected and infected with a closely related strain of HCV genotype 4d...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077590/molecular-epidemiology-of-ascaris-infection-among-pigs-in-iowa
#6
Jeba Jesudoss Chelladurai, Kaitlyn Murphy, Tymbrie Snobl, Christopher Bader, Cody West, Kylie Thompson, Matthew T Brewer
Ascaris is a large roundworm parasite that infects humans and pigs throughout the world. Molecular markers have been used to study parasite transmission in Ascaris-endemic and -nonendemic regions of the world. In the United States, ascariasis still persists in commercial swine and has been designated a neglected disease of poverty in humans. However, relatively few data are available for evaluation of zoonotic transmission. In the present study, we obtained adult worms from abattoirs and characterized each worm on the basis of the gene encoding nuclear internal transcribed sequence (ITS) and mitochondrial cox1 Restriction fragment-length polymorphism analysis of ITS revealed swine, human, and hybrid genotypes...
January 1, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28077191/genome-wide-analysis-in-endangered-populations-a-case-study-in-barbaresca-sheep
#7
S Mastrangelo, B Portolano, R Di Gerlando, R Ciampolini, M Tolone, M T Sardina
Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data...
January 12, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28074554/population-genetic-analysis-of-giardia-duodenalis-genetic-diversity-and-haplotype-sharing-between-clinical-and-environmental-sources
#8
Mauricio Durigan, Maisa Ciampi-Guillardi, Ricardo C A Rodrigues, Juliane A Greinert-Goulart, Isabel C V Siqueira-Castro, Diego A G Leal, Sandra Yamashiro, Taís R Bonatti, Maria I Zucchi, Regina M B Franco, Anete P de Souza
Giardia duodenalis is a flagellated intestinal protozoan responsible for infections in various hosts including humans and several wild and domestic animals. Few studies have correlated environmental contamination and clinical infections in the same region. The aim of this study was to compare groups of Giardia duodenalis from clinical and environmental sources through population genetic analyses to verify haplotype sharing and the degree of genetic similarity among populations from clinical and environmental sources in the metropolitan region of Campinas...
January 11, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28073995/a-pericentric-inversion-of-chromosome-x-disrupting-f8-and-resulting-in-haemophilia-a
#9
Yu Xin, Jingyi Zhou, Qiulan Ding, Changming Chen, Xi Wu, Xuefeng Wang, Hongli Wang, Xiaofeng Jiang
AIMS: The frequency of X chromosome pericentric inversion is much less than that of autosome chromosome. We hereby characterise a pericentric inversion of X chromosome associated with severe factor VIII (FVIII) deficiency in a sporadic haemophilia A (HA) pedigree. METHODS: PCR primer walking and genome walking strategies were adopted to identify the exact breakpoints of the inversion. Copy number variations (CNVs) of the F8 and the whole chromosomes were detected by AccuCopy and Affymetrix CytoScan High Definition (HD) assays, respectively...
January 10, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28073605/comprehensive-association-analysis-of-27-genes-from-the-gabaergic-system-in-japanese-individuals-affected-with-schizophrenia
#10
Shabeesh Balan, Kazuo Yamada, Yoshimi Iwayama, Takanori Hashimoto, Tomoko Toyota, Chie Shimamoto, Motoko Maekawa, Shu Takagai, Tomoyasu Wakuda, Yosuke Kameno, Daisuke Kurita, Kohei Yamada, Mitsuru Kikuchi, Tasuku Hashimoto, Nobuhisa Kanahara, Takeo Yoshikawa
Involvement of the gamma-aminobutyric acid (GABA)-ergic system in schizophrenia pathogenesis through disrupted neurodevelopment has been highlighted in numerous studies. However, the function of common genetic variants of this system in determining schizophrenia risk is unknown. We therefore tested the association of 375 tagged SNPs in genes derived from the GABAergic system, such as GABAA receptor subunit genes, and GABA related genes (glutamate decarboxylase genes, GABAergic-marker gene, genes involved in GABA receptor trafficking and scaffolding) in Japanese schizophrenia case-control samples (n=2926; 1415 cases and 1511 controls)...
January 7, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28073527/new-scenario-for-speciation-in-the-benthic-dinoflagellate-genus-coolia-dinophyceae
#11
Chui Pin Leaw, Toh Hii Tan, Hong Chang Lim, Sing Tung Teng, Hwa Lin Yong, Kirsty F Smith, Lesley Rhodes, Matthias Wolf, William C Holland, Mark W Vandersea, R Wayne Litaker, Patricia A Tester, Haifeng Gu, Gires Usup, Po Teen Lim
In this study, inter- and intraspecific genetic diversity within the marine harmful dinoflagellate genus Coolia Meunier was evaluated using isolates obtained from the tropics to subtropics in both Pacific and Atlantic Ocean basins. The aim was to assess the phylogeographic history of the genus and to clarify the validity of established species including Coolia malayensis. Phylogenetic analysis of the D1-D2 LSU rDNA sequences identified six major lineages (L1-L6) corresponding to the morphospecies Coolia malayensis (L1), C...
May 2016: Harmful Algae
https://www.readbyqxmd.com/read/28070706/analysis-of-12-x-str-loci-in-the-population-of-south-croatia
#12
Gordan Mršić, Petar Ozretić, Josip Crnjac, Siniša Merkaš, Ivana Račić, Sara Rožić, Viktorija Sukser, Maja Popović, Marina Korolija
The aim of the study was to assess forensic pertinence of 12 short tandem repeats (STRs) on X-chromosome in south Croatia population. Investigator(®) Argus X-12 kit was used to co-amplify 12 STR loci belonging to four linkage groups (LGs) on X-chromosome in 99 male and 98 female DNA samples of unrelated donors. PCR products were analyzed by capillary electrophoresis. Population genetic and forensic parameters were calculated by the Arlequin and POPTREE2 software, and an on-line tool available at ChrX-STR.org...
January 9, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28069403/functional-variant-in-the-promoter-region-of-il-27-alters-gene-transcription-and-confers-a-risk-for-ulcerative-colitis-in-northern-chinese-han
#13
Wei Yu, Kun Zhang, Zhongyi Wang, Jiayu Zhang, Tong Chen, Lifang Jin
Ulcerative colitis (UC) is a chronic inflammatory disorder of unknown etiology and a polygenic disease. IL-27 encodes p28, a subunit of IL-12 family cytokines, and has been implicated in the pathogenesis of UC. The aims of the present study were to evaluate the genetic association of a variant of the IL-27 gene with UC and to further characterize the functional variant in the IL-27 gene that influences the risk for UC. Our data demonstrated that the genetic variant rs153109 in the 5' upstream region of IL-27 is significantly associated with UC in Chinese Han individuals...
January 6, 2017: Human Immunology
https://www.readbyqxmd.com/read/28069185/combination-of-uterine-natural-killer-cell-immunoglobulin-receptor-haplotype-and-trophoblastic-hla-c-ligand-influences-the-risk-of-pregnancy-loss-a-retrospective-cohort-analysis-of-direct-embryo-genotyping-data-from-euploid-transfers
#14
Scott J Morin, Nathan R Treff, Xin Tao, Richard T Scott, Jason M Franasiak, Caroline R Juneau, Marcy Maguire, Richard T Scott
OBJECTIVE: To compare maternal uterine natural killer cell immunoglobulin receptor (KIR) genotype and haplotype frequencies between patients whose euploid single-embryo transfer resulted in pregnancy loss and those that resulted in delivery and to determine if the risk of pregnancy loss was affected by the HLA-C genotype content in the embryo. DESIGN: Retrospective cohort. SETTING: Academic research center. PATIENT(S): Autologous fresh IVF cycles resulting in positive serum β-hCG during 2009-2014...
January 6, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28068531/forensic-data-and-microvariant-sequence-characterization-of-27-y-str-loci-analyzed-in-four-eastern-african-countries
#15
Giuseppe Iacovacci, Eugenia D'Atanasio, Ornella Marini, Alfredo Coppa, Daniele Sellitto, Beniamino Trombetta, Andrea Berti, Fulvio Cruciani
By using the recently introduced 6-dye Yfiler(®) Plus multiplex, we analyzed 462 males belonging to 20 ethnic groups from four eastern African countries (Eritrea, Ethiopia, Djibouti and Kenya). Through a Y-STR sequence analysis, combined with 62 SNP-based haplogroup information, we were able to classify observed microvariant alleles at four Y-STR loci as either monophyletic (DYF387S1 and DYS458) or recurrent (DYS449 and DYS627). We found evidence of non-allelic gene conversion among paralogous STRs of the two-copy locus DYF387S1...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28068530/a-new-view-on-the-european-feline-population-from-mtdna-analysis-in-polish-domestic-cats
#16
Iwona Głażewska, Tomasz Kijewski
Domestic cats from Eastern Europe have been poorly represented in studies on mitochondrial DNA diversity for forensic purposes until now. The aim of the present study was to contribute to closing this gap. The genetic structure and the origin of a cat population in Poland were examined against the background of human migrations over the centuries. One hundred and eighty-one cats from animal shelters in seven cities were genotyped. Twenty-one mtDNA haplotypes were found, with only one haplotype present in each of the populations, at an average frequency of 63...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28068523/rs12941170-at-sox9-gene-associated-with-orofacial-clefts-in-chinese
#17
Zhong-Lin Jia, Sha He, Shu-Yuan Jiang, Bi-He Zhang, Shi-Jun Duan, Jia-Yu Shi, Ning Huang, Wen-Chao Zhu, Bing Shi
OBJECTIVE: Non-syndromic orofacial cleftings (NSOCs) are considered as complex trait, which results from genetic and/or environmental modifiers. Current findings could only explain small portion of the NSOCs. SOX9 gene plays an important role during craniofacial development in animal models and the Pierre Robin sequence (PRS). However, its role in non-syndromic clefts remains unknown. DESIGN: In this study, we selected eight SNPs in and around SOX9 gene to make maximum coverage, and genotyped them by using RFLP-PCR and ligase detection reaction (LDR) methods to test its associations among 151 NSOCs (53 NSCLP, 52 NSCLO and 46 NSCPO) from Western Han Chinese population...
December 30, 2016: Archives of Oral Biology
https://www.readbyqxmd.com/read/28067456/type-2-diabetes-mellitus-associated-with-the-interaction-of-lrp5-polymorphism-and-overweight-and-obesity-in-rural-chinese-adults
#18
Zhang Lu, Wang Jinjin, Zhang Ming, Wang Guo'an, Shen Yanxia, Wu Dongting, Wang Chongjian, Li Linlin, Ren Yongcheng, Wang Bingyuan, Zhang Hongyan, Yang Xiangyu, Zhao Yang, Han Chengyi, Zhou Junmei, Pang Chao, Yin Lei, Zhao Jingzhi, Luo Xinping, Hu Dongsheng
BACKGROUND: Low-density lipoprotein receptor-related protein 5 (LRP5) plays an important role in glucose and cholesterol metabolism, so a cohort study was used to evaluate the association of LRP5 variants and incidence of type 2 diabetes mellitus (T2DM) in a rural adult Chinese population. METHODS: A total of 7751 subjects ≥18 years old and without T2DM underwent genotyping at baseline; 6326 subjects (81.62%) were followed-up, with 5511 eligible for this analysis...
January 9, 2017: Journal of Diabetes
https://www.readbyqxmd.com/read/28064470/genome-wide-association-study-discovered-genetic-variation-and-candidate-genes-of-fibre-quality-traits-in-gossypium-hirsutum-l
#19
Zhengwen Sun, Xingfen Wang, Zhengwen Liu, Qishen Gu, Yan Zhang, Zhikun Li, Huifeng Ke, Jun Yang, Jinhua Wu, Liqiang Wu, Guiyin Zhang, Caiying Zhang, Zhiying Ma
Genetic improvement of fibre quality is one of the main breeding goals for the upland cotton, Gossypium hirsutum, but there are difficulties with precise selection of traits. Therefore, it is important to improve the understanding of the genetic basis of phenotypic variation. In this study, we conducted phenotyping and genetic variation analyses of 719 diverse accessions of upland cotton based on multiple environment tests and a recently developed Cotton 63K Illumina Infinium SNP array and performed a genome-wide association study (GWAS) of fibre quality traits...
January 8, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28062664/mapping-eqtls-with-rna-seq-reveals-novel-susceptibility-genes-non-coding-rnas-and-alternative-splicing-events-in-systemic-lupus-erythematosus
#20
Christopher A Odhams, Andrea Cortini, Lingyan Chen, Amy L Roberts, Ana Viñuela, Alfonso Buil, Kerrin S Small, Emmanouil T Dermitzakis, David L Morris, Timothy J Vyse, Deborah S Cunninghame Graham
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines...
January 5, 2017: Human Molecular Genetics
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